Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
This variantScenario
BenignPathogenic
Uncertain.The recorded classification is uncertain significance.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
About POLE
POLE encodes the catalytic subunit of DNA polymerase epsilon, the enzyme that replicates the leading strand of DNA during cell division and participates in DNA repair. It contains a proofreading domain that corrects replication errors, keeping the accumulation of mutations in check. Germline mutations in POLE cause polyposis and predispose to colorectal cancer, and are also linked to a rare syndrome of facial dysmorphism, immunodeficiency, livedo, and short stature. Somatic mutations, particularly in the proofreading domain, occur in colorectal and endometrial cancers, where they drive an ultra-mutated tumor phenotype and are associated with better responses to immune checkpoint inhibitors.
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Criteria may be applied incorrectly, sources may be misread, and a
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Double-check every criterion and its underlying evidence
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01The reasoning
How it was classified
The recorded framework is León-Castillo et al. 2020 custom POLE framework. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Met (Supporting): gnomAD allele frequency 0.0008% (v2.1) and 0.00043% (v4.1) with zero homozygotes, below the 0.1% PM2 threshold.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Uncertain significance
VUS: only PM2 (Supporting) is met - gnomAD allele frequency 0.0008% (v2.1) with zero homozygotes - and that satisfies no pathogenic, likely-pathogenic, or benign combination under the ACMG/AMP 2015 rules. Flagged for human review: an unverifiable functional-study assertion and an incomplete same-residue variant search could change the call.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
7 / 1,613,882 alleles
gnomAD v4.1: 7 / 1,613,882 alleles. Recorded AF 4.33737e-06. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 7.95469e-06; MAF= 0.00080%, 2/251424 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26627e-05; MAF= 0.00327%, 1/30616 alleles, homozygotes = 0).
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. POLE, the catalytic subunit of DNA polymerase epsilon, is an enzyme involved in DNA replication and repair. Select POLE mutations lead to ultra-high m
ACMG/AMP criteria under León-Castillo et al. 2020 custom POLE framework, with the data and sources behind each one.
28 criteria with recorded statuses: 1 met · 11 not met · 12 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Consequence adjudication for NM_006231.4:c.2284C>T (POLE): the variant is a single-nucleotide substitution producing missense change NP_006222.2:p.(Arg762Trp) in exon 20 of 49 of the MANE Select transcript NM_006231.4 (VariantValidator/Mutalyzer).
No null-variant consequence exists: the variant is not a nonsense, frameshift, canonical splice-site, or initiation-codon variant; SpliceAI max delta score = 0.00 predicts no splice disruption; as a missense variant it does not trigger NMD and is not predicted to truncate the protein.
Protein length is unchanged: substitution at residue 762 of the 2286-residue NP_006222.2 protein; no in-frame indel or stop-loss consequence, so PM4 is not applicable.
No repeat-region context and no indel consequence, so BP3 is not applicable.
Framework: no ClinGen CSPEC exists for POLE (cspec.found=false). The local custom POLE framework (Leon-Castillo et al. 2020, custom_internal) customizes only PM1, PS4, PP3, and BP4; PVS1 therefore falls back to the generic ClinGen SVI framework (PMC6185798) and PM4/BP3 to generic ACMG/AMP 2015 (PMID 25741868). All three criteria are categorically excluded for this missense variant regardless of framework choice.
PS1 not_met: c.2284C>T is the only nucleotide change producing p.Arg762Trp (c.2284 is the first base of codon 762, CGG); no source establishes p.Arg762Trp or any Arg762 substitution as pathogenic (ClinVar VUS x3 labs, OncoKB unknown effect, no variant-specific literature).
PM1 not_met: the governing León-Castillo 2020 custom framework restricts PM1 to exact exonuclease-domain substitutions (hotspots P286R/V411L/S297F/A456P/S459F and listed recurrent variants); p.R762W is in no list, is absent from the entire paper and all supplementary tables, is not a Cancer Hotspots hit, and has only 1 somatic COSMIC occurrence (non-recurrent per the paper's own definition). Generic ACMG/AMP 2015 PM1 fallback also not met.
PM5 not_assessed: pm5_candidates artifact harvested 0 same-residue comparator candidates in 'unknown' mode and explicitly requires manual review; no dedicated survey of other substitutions at Arg762 was performed.
PP2 not_assessed: missense-common-mechanism component is supported for POLE, but the low-rate-of-benign-missense-variation component has no gene-level constraint data (no gnomAD missense Z-score/oe with named source, no HCI prior) in the case evidence; both prongs are required.
BP1 not_met: POLE disease is driven by missense (exonuclease domain), not primarily truncating variants, so BP1 cannot apply to a POLE missense variant.
No criterion in this group was inferred from any source's final classification; ClinVar VUS was used only as factual absence-of-established-pathogenic evidence.
No ClinGen CSPEC exists for POLE; the local custom framework (León-Castillo et al. 2020, vcep_path_250_323) customizes only PM1, PS4, PP3, and BP4, so PS2, PM6, PP1, and BS4 are governed by generic ACMG/AMP 2015 (Richards et al., PMID 25741868).
The case evidence bundle contains no proband-parental trio data, no de novo occurrence data, no parental testing, no mosaicism assessment, and no family segregation data for NM_006231.4:c.2284C>T (p.Arg762Trp).
ClinVar VCV000420873 (3 germline submissions, all Uncertain significance, 2-star) provides no de novo or segregation assertions; PMID:28492532 full text is empty in this case bundle; PMID:25394175 is a referral-indications guideline with no variant-specific content.
All four criteria in this group are returned as not_assessed due to absent evidence; no criterion can be met, and no benign/negative inference (e.g., BS4 from absent data) is drawn.
PS3 and BS3 are both not_assessed: the case bundle contains no functional assay evidence of any direction for POLE p.Arg762Trp (c.2284C>T). The absence of functional data contributes no pathogenic (PS3) or benign (BS3) weight to the classification; any functional evidence would need to be supplied or located before either criterion can be applied.
No ClinGen CSPEC is available for POLE (cspec.found=false); the governing framework is the local custom POLE framework derived from Leon-Castillo et al. 2020 (J Pathol 250:323-335), which customizes PS4 (somatic-recurrence adaptation capped at Supporting). PP4, PP5, BP5, and BP6 are not customized by that framework and fall back to generic ACMG/AMP 2015 (Richards et al. 2015, PMID 25741868).
PS4: not met. p.Arg762Trp is absent from Supplementary Table S1 (recurrent COSMIC+TCGA EC variants; 101 rows verified), is not in the established pathogenic hotspot set (P286R, V411L, A456P, S297F), and has only a single somatic COSMIC observation (n=1, COSV57690452). No germline case-control or enrichment data exist, so neither the custom PS4 rule nor generic PS4 is satisfied.
PP4: not assessed. The bundle contains no proband phenotype or family history data; ClinVar condition labels ('Hereditary cancer-predisposing syndrome', 'not provided') are nonspecific and cannot establish a phenotype highly specific for POLE.
PP5: not met. ClinVar variation 420873 is 'Uncertain significance' (2 stars) from 3 single-submitter laboratories with zero expert-panel submissions; no exact-variant expert-panel Pathogenic/Likely pathogenic classification exists, which is the sole permitted trigger for PP5.
BP6: not met. No exact-variant ClinVar expert-panel Benign/Likely benign classification exists; the aggregate 2-star VUS label is expressly excluded as a BP6 trigger.
BP5: not assessed. No proband-level case data are available to document an alternate molecular basis of disease.
Both bundled full-text publications (PMID:25394175, PMID:28492532) were reviewed; neither mentions c.2284C>T/p.Arg762Trp (they are a cancer-referral practice guideline and the Sherloc criteria-methodology paper), so neither provides variant-specific support for any criterion in this group.
PM3 and BP2 are phase-dependent criteria. The case bundle contains no proband-level phase, pedigree, or segregation data, so both are returned as not_assessed with the data gap explicitly identified.
Inheritance-mode analysis: POLE germline cancer predisposition (polymerase proofreading-associated polyposis, OMIM 615083) is autosomal dominant, making PM3's recessive premise inapplicable in this case context unless a recessive presentation (e.g., FILS syndrome, OMIM 615139) is documented; no such documentation exists in the case materials.
Neither retrieved publication (ACMG/NSGC referral-indications guideline, PMID 25394175; Sherloc framework paper, PMID 28492532) mentions c.2284C>T / p.(Arg762Trp) or provides any cis/trans observation; ClinVar submissions for the variant are all Uncertain significance with no phase data reported.
No pathogenic variant in trans or cis with this variant is documented anywhere in the evidence bundle; until phase and a co-occurring variant are established, both allelic criteria remain unevaluable.
PP3: not met. Custom POLE framework PP3 rule not triggered (c.2284C>T/p.R762W absent from Supp Tables S2 and S3, verified in the xlsx files); generic fallback yields no PP3: REVEL 0.552 is in the SVI-indeterminate range (PMID 36413997), SpliceAI max delta 0.00 is below the 0.2 splice-impact threshold (PMID 37352859), and BayesDel has no verified published calibration threshold.
BP4: not met. Custom POLE framework BP4 rule not triggered (variant absent from Supp Tables S2/S3); generic fallback yields no BP4: REVEL 0.552 is far above the <=0.016 BP4 threshold (PMID 36413997), BayesDel is insufficiently calibrated, and low SpliceAI delta is not BP4 evidence for a missense variant.
BP7: not applicable. The variant is missense (p.Arg762Trp); BP7 is restricted to synonymous variants with no predicted splice impact.
No publication in this case's bundle mentions the variant (25394175, 28492532 screened for 'R762/Arg762/c.2284/2284C': 0 hits), so no paper is cited for these criteria; thresholds are cited from their named calibration publications (PMID 36413997, PMID 37352859).
ClinVar submission SCV005928891 (Ambry) reports an in-silico PP3 signal ('the in silico prediction for this alteration is inconclusive'); this was not used, because criterion evidence is not inferred from another submitter's classification, and the directly evaluated calibrated predictors here do not meet PP3/BP4 thresholds.
Governing framework: ClinGen CSPEC not found for POLE; local custom gene framework (León-Castillo et al. 2020 custom POLE framework, framework_mode custom_gene_framework) is in force but customizes only PM1, PS4, PP3 and BP4. It contains no population-frequency rules, so BA1/BS1/BS2/PM2 were adjudicated under the generic ACMG/AMP fallback (Richards et al. 2015, PMID 25741868) with the project's adopted non-VCEP gnomAD thresholds: PM2 AF <0.1%, BS1 AF >0.3%, BA1 AF >1%.
Population data: gnomAD v2.1 total AF 0.0008% (2/251,424, 0 homozygotes, max subpopulation SAS 0.0033%) and gnomAD v4.1 total AF 0.00043% (7/1,613,882, 0 homozygotes, grpmax FAF 0.00018%, max subpopulation SAS 0.0011%). The variant is ultra-rare with no homozygotes in either dataset.
Outcome: BA1 not met (AF 2-4 orders of magnitude below threshold), BS1 not met (AF ~100-fold below threshold), BS2 not met (0 homozygotes; only 7 ultra-rare heterozygotes; no phenotype-verified healthy adult cohort), PM2 met at Supporting strength (AF well below 0.1% in both datasets).
No population criterion was inferred from any other source's final classification; ClinVar (VUS, 3 laboratories) was not used as population evidence.
Ancestry consideration: the highest AF is in South Asians in both datasets (0.0033% v2.1, 0.0011% v4.1); even the highest-ancestry AF remains far below BS1/BA1 thresholds, so the conclusions are ancestry-robust.
No criteria match.
Met · 1
PM2SupportingMet (Supporting): gnomAD allele frequency 0.0008% (v2.1) and 0.00043% (v4.1) with zero homozygotes, below the 0.1% PM2 threshold.
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Reasoning
PM2 is met: the variant is present at extremely low frequency (or near-absent) in large population cohorts. gnomAD v2.1 AF 0.0008% (2/251,424, 0 homozygotes) and gnomAD v4.1 AF 0.00043% (7/1,613,882, 0 homozygotes) are both well below the project generic-fallback PM2 threshold of AF <0.1% for non-VCEP gnomAD; the v4.1 grpmax filtering allele frequency is 0.00018%, also far below threshold. No homozygotes were observed in either dataset. For this autosomal dominant cancer-predisposition phenotype (rare, incomplete penetrance), a maximum credible population AF well below 0.1% is expected, and the observed AF is consistent with a rare disease-associated variant. PM2 is applied at Supporting strength, per the ClinGen SVI recommendation to weight PM2 as supporting evidence (as operationalized in Bayesian calibration of the ACMG/AMP framework).
Rule
PM2 (Supporting): absent or extremely low allele frequency in large population cohorts - project generic ACMG/AMP fallback threshold for non-VCEP genes: AF <0.1% in gnomAD (Richards et al. 2015, PMID 25741868; Whiffin et al. 2017, PMID 28518168); strength Supporting per ClinGen SVI recommendation (Tavtigian et al. 2018, PMID 29565419)
Evidence considered
gnomAD v2.1 AF 7.95469e-06 (0.0008%, 2/251,424, 0 homozygotes) - below the PM2 threshold of AF <0.1% for non-VCEP gnomAD (maximum credible AF framework, Whiffin et al. 2017, PMID 28518168; PM2 'absent/extremely low frequency' definition, Richards et al. 2015, PMID 25741868)
gnomAD v4.1 AF 4.33737e-06 (0.00043%, 7/1,613,882, 0 homozygotes), grpmax FAF 1.83e-06 (0.00018%) - below the PM2 threshold of AF <0.1% (Whiffin et al. 2017, PMID 28518168; Richards et al. 2015, PMID 25741868)
PM2 applied at Supporting strength per ClinGen SVI general recommendation weighting PM2 as supporting evidence, consistent with the Bayesian calibration of ACMG/AMP criterion weights (Tavtigian et al. 2018, PMID 29565419)
Still missing
gnomAD v4.1 top-level genome AC/AN fields were 0/0 in the retrieved record; total AF reflects the joint exome+genome dataset, so a separate genome-only frequency could not be inspected
gnomAD-Canada (HostSeq) not retrieved; an independent Canadian cohort would add corroboration
PS1Not met: no source establishes any Arg762 substitution as pathogenic, and no alternative nucleotide change at this codon produces Trp.
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Reasoning
PS1 (same amino acid change as a previously established pathogenic variant, regardless of nucleotide change) is not met. The variant is NM_006231.4:c.2284C>T, p.(Arg762Trp). c.2284 is the first base of codon 762 (CGG); the only nucleotide change that produces Trp at residue 762 is C>T itself (C>A would be synonymous, C>G would give Gly), so there is no alternative nucleotide change to compare. No collected source establishes p.Arg762Trp (or any Arg762 substitution) as pathogenic: ClinVar record 420873 is Uncertain significance from 3 clinical laboratories (no expert panel submissions); OncoKB lists R762W as 'Unknown Oncogenic Effect' with no variant-specific reviewed functional evidence; the only two retrieved publications (PMID:25394175, PMID:28492532) contain zero variant-specific content (full-text search for R762/Arg762/2284/POLE returned no hits); and the León-Castillo 2020 custom framework's established pathogenic POLE missense set does not include residue 762 (the paper text contains no occurrence of '762' at all). Absence of an established pathogenic same-amino-acid change therefore fails PS1. Per instruction, the ClinVar VUS final classification itself was not used as criterion evidence, only the factual absence of any established pathogenic classification of this exact change in collected sources.
Rule
Generic ACMG/AMP 2015 PS1 (PMID 25741868); no POLE-specific PS1 specification exists in the governing custom framework
Evidence considered
clinvar - ClinVar variation 420873: p.Arg762Trp classified Uncertain significance by 3 clinical laboratories; no expert panel submission establishes this exact amino-acid change as pathogenic (used only as absence-of-established-pathogenic evidence, not as a criterion inference)
vcep_path_250_323 - León-Castillo et al. 2020 (J Pathol 250:323-335): established pathogenic POLE exonuclease-domain missense set (P286R, V411L, S297F, A456P, S459F) does not include residue 762; '762' does not appear anywhere in the paper
PMID:25394175 - Hampel et al. 2015 ACMG/NSGC referral guideline; full text searched, no variant-specific content
PMID:28492532 - Nykamp et al. 2017 Sherloc; full text searched, no variant-specific content
PS4Not met: the variant is absent from the framework's recurrent-variant table and has only a single somatic COSMIC occurrence (n=1), which is not recurrence.
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Reasoning
No ClinGen CSPEC exists for POLE; the governing framework is the local custom POLE framework derived from Leon-Castillo et al. 2020 (J Pathol 250:323-335), which customizes PS4 as a somatic-recurrence adaptation capped at Supporting. That rule triggers only for an exact missense variant that is recurrent in BOTH the COSMIC and TCGA endometrial carcinoma cohorts in Supplementary Table S1, has a combined EC count >=10, and belongs to the established/pathogenic set (p.P286R, p.V411L, p.A456P, p.S297F). p.Arg762Trp (c.2284C>T) satisfies none of these: (1) it is absent from Supplementary Table S1 entirely (verified across all 101 rows of the recurrent-variant table, whose top entries are P286R=181, V411L=114, A456P=20, S297F=18); (2) it is not one of the established hotspot substitutions; (3) the only somatic observation is a single COSMIC entry (COSV57690452, n=1, from evidence.json), which is not recurrence and is somatic, not germline case-control evidence. No germline case-control or cohort-enrichment study for this exact variant is present in the case bundle, and ClinVar contains only 3 single-submitter VUS submissions with no enrichment data. Generic ACMG/AMP 2015 PS4 (higher prevalence in affected individuals vs controls) is likewise unsupported. PS4 therefore not met at any strength.
Rule
Custom POLE framework (Leon-Castillo 2020-derived, PS4 customized): 'Apply PS4_Supporting only when the exact POLE missense variant is recurrent in both the COSMIC and TCGA endometrial carcinoma cohorts in Supplementary Table S1, has a combined EC count >=10, and belongs to the established/pathogenic set highlighted by Leon-Castillo et al. 2020. Under the current package this supports p.P286R, p.V411L, p.A456P, and p.S297F. Do not upgrade above Supporting.' Fallback generic ACMG/AMP 2015 PS4 (Richards et al. 2015, PMID 25741868) applies outside the custom rule and is also unmet.
Evidence considered
vcep_path_250_323_s002
vcep_path_250_323
clinvar
generic_acmg_combination_rules
Still missing
No germline case-control or cohort-enrichment studies for c.2284C>T (p.Arg762Trp) were identified in the case bundle
Variant is absent from Supplementary Table S1 (recurrent COSMIC/TCGA EC variants), so the custom framework's recurrence preconditions (recurrent in both cohorts, combined EC count >=10) cannot be met
Only a single somatic COSMIC observation (n=1, COSV57690452) exists; no EC proband counts are available
PM1Not met: Arg762 lies outside the framework's exonuclease-domain hotspot region (residues 286-459) and in none of its hotspot lists.
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Reasoning
PM1 (mutational hotspot or critical/well-established functional domain without benign variation) is not met. The governing framework is the local custom León-Castillo et al. 2020 POLE framework (no official ClinGen CSPEC/VCEP exists for POLE). Its PM1 rules are exact-substitution lists: PM1_Strong for p.P286R, p.V411L, p.S297F, p.A456P, p.S459F; PM1_Moderate for p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, p.D368Y; PM1_Supporting for p.A465V, p.L424V, p.T278M, p.A428T. The framework explicitly restricts these to the exact substitutions listed ('not all substitutions at the same codon') and instructs generic ACMG/AMP fallback outside the explicit rules. p.R762W is in none of the lists. The framework's own instruments confirm non-eligibility: the paper text contains no occurrence of '762' (verified by full-text extraction of PATH-250-323.pdf), and none of the supplementary tables S1/S2/S3 (PATH-250-323-s002/-s003/-s004.xlsx) contains a row for p.R762W/c.2284C>T. Under generic ACMG/AMP 2015 PM1, the variant is not a mutational hotspot: Cancer Hotspots reports no statistically significant hotspot at POLE R762, and COSMIC shows a single somatic occurrence (COSV57690452, n=1), which the paper itself defines as non-recurrent ('considered non-recurrent if it was found only once'; recurrent = present in two or more samples in COSMIC and/or TCGA). R762 lies outside the exonuclease-domain hotspot region addressed by the framework (hotspots at residues 286-459), and no source in this case establishes residue 762 as a critical/well-studied functional domain position without benign variation.
Rule
León-Castillo 2020 custom PM1 (exact-substitution lists; p.R762W not listed) with fallback to generic ACMG/AMP 2015 PM1 (PMID 25741868)
Evidence considered
vcep_path_250_323 - León-Castillo et al. 2020: the five established exonuclease-domain hotspots are P286R, V411L, S297F, A456P, S459F; recurrence defined as >=2 samples in COSMIC/TCGA; 'considered non-recurrent if it was found only once'; full text contains no occurrence of '762'
vcep_path_250_323_s002 - Supplementary Table S1 (recurrent POLE variants, COSMIC + TCGA EC cohorts, 101 rows): no row for p.R762W / c.2284C>T
vcep_path_250_323_s003 - Supplementary Table S2 (TCGA in silico results): no row for p.R762W / c.2284C>T
vcep_path_250_323_s004 - Supplementary Table S3 (non-TCGA EC cohort in silico results): no row for p.R762W / c.2284C>T
oncokb - OncoKB R762W 'Unknown Oncogenic Effect', no hotspot/domain-level pathogenic annotation for this residue
Generic ACMG/AMP 2015 PM1 fallback (Richards et al. 2015, PMID 25741868) per custom-framework note that rules outside the explicit León-Castillo lists fall back to generic ACMG/AMP
evidence.json 'hotspots' result (Cancer Hotspots: no statistically significant hotspot at POLE R762) and 'cosmic' result (COSV57690452, somatic count 1) - referenced in prose only; these two results have no source_registry keys (see warnings)
Still missing
No official ClinGen CSPEC/VCEP for POLE; the custom framework's PM1 rules cover only exact exonuclease-domain substitutions, so polymerase-domain residue 762 PM1 status rests on generic ACMG/AMP with no domain-level functional annotation retrieved for this residue
PP3Not met: REVEL 0.552 falls in the indeterminate range (PP3 requires >=0.932), and SpliceAI max delta 0.00 shows no splice impact.
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Reasoning
Variant NM_006231.4:c.2284C>T (POLE, p.Arg762Trp) is a missense variant in exon 20. The governing local custom POLE framework (Leon-Castillo et al. 2020, PATH-250-323) pre-assigns PP3_Supporting only when the exact variant appears in Supplementary Table S2 or S3 with REVEL class 'likely disease causing' and <=1 benign in silico result; direct inspection of PATH-250-323-s003.xlsx (Table S2) and PATH-250-323-s004.xlsx (Table S3) shows the variant is absent from both tables (and from Table S1), so the custom rule is not triggered and the framework mandates fallback to the generic in-silico workflow. Under generic fallback: (1) REVEL score = 0.552; per ClinGen SVI calibration (Pejaver et al. 2022, PMID 36413997) REVEL >= 0.932 supports PP3 and <= 0.016 supports BP4, so 0.552 lies in the indeterminate range and provides no PP3 support; (2) SpliceAI max delta = 0.00 (pangolin_SG 0.0, pangolin_SL -0.01), well below the delta >= 0.2 splice-impact threshold of the ClinGen SVI Splicing Subgroup (Walker et al. 2023, PMID 37352859), so the splice path provides no PP3 support; (3) BayesDel score = 0.0523 cannot be used because no verified published calibration threshold (publication + table) is available, per pipeline policy. No computational evidence path meets the PP3 threshold.
Rule
Custom POLE PP3 rule (exact variant in Supp Table S2/S3 + REVEL 'likely disease causing' + <=1 benign tool) NOT triggered (variant absent); generic fallback: REVEL >=0.932 (PMID 36413997) or SpliceAI delta >=0.2 (PMID 37352859) required for PP3
Evidence considered
REVEL score 0.552 for NM_006231.4:c.2284C>T (p.Arg762Trp); ClinGen SVI calibration (Pejaver et al. 2022, Am J Hum Genet, PMID 36413997) recommends REVEL >=0.932 for PP3 and <=0.016 for BP4; 0.552 is indeterminate -> no PP3 support.
SpliceAI max delta score = 0.00 (pangolin_SG 0.0, pangolin_SL -0.01); ClinGen SVI Splicing Subgroup recommendations (Walker et al. 2023, Am J Hum Genet, PMID 37352859) require delta >=0.2 for splice-impact PP3; 0.00 provides no PP3 support.
BayesDel score 0.0523 (local lookup); no verified published calibration threshold (named publication and table) is available, so the score is treated as insufficiently calibrated and cannot support PP3.
Custom POLE framework (PATH-250-323, Leon-Castillo et al. 2020) PP3_Supporting rule requires the exact variant in Supplementary Table S2 or S3 with REVEL class 'likely disease causing' and <=1 benign in silico result; c.2284C>T/p.R762W is absent from PATH-250-323-s003.xlsx and PATH-250-323-s004.xlsx (verified by direct row inspection), so the rule is not triggered and generic fallback applies.
Still missing
Variant absent from POLE framework Supplementary Tables S2/S3, so the table-grounded custom PP3 rule could not be applied
BayesDel score 0.0523 treated as insufficiently calibrated: no verified published threshold (PMID + table) available to this pipeline
REVEL 0.552 falls in the ClinGen SVI indeterminate range (0.016-0.932), providing no PP3 support
PP5Not met: ClinVar lists only Uncertain significance from three clinical laboratories, with no expert-panel pathogenic classification.
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Reasoning
PP5 was evaluated strictly per the group instruction: it may be triggered ONLY by an exact-variant ClinVar expert-panel classification of Pathogenic/Likely pathogenic; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger it. For NM_006231.4:c.2284C>T (ClinVar variation 420873), the ClinVar record shows an aggregate classification of 'Uncertain significance' (review stars 2, 'criteria provided, multiple submitters, no conflicts'), with expert_panels empty and 0 expert-panel submissions; all three submissions are single-submitter clinical laboratories (GeneDx, Labcorp/Invitae, Ambry) each classifying the variant as VUS. No expert-panel Pathogenic/Likely pathogenic classification exists for this exact variant, so PP5 is not met. The two bundled publications (PMID:25394175, PMID:28492532) were reviewed and neither mentions this variant; they are a cancer-referral practice guideline and a variant-classification methodology paper respectively, and cannot serve as a 'reputable source' report of pathogenicity for this exact variant.
Rule
Generic ACMG/AMP 2015 PP5 (reputable source recently reports variant as pathogenic, evidence not available to the laboratory for independent evaluation), restricted per group instruction to exact-variant ClinVar expert-panel Pathogenic/Likely pathogenic classifications only.
Evidence considered
clinvar
generic_acmg_combination_rules
Still missing
No ClinVar expert-panel (3-star) classification exists for this variant; only 3 single-submitter laboratory VUS submissions are present
No reputable-source publication reports this exact variant as pathogenic
BA1Not met: the highest observed allele frequency is 0.00327%, versus the >1% BA1 threshold.
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Reasoning
BA1 requires an allele frequency too high for the disorder. Under the project generic ACMG/AMP fallback for non-VCEP genes, the BA1 threshold is AF >1% in gnomAD (the original Richards et al. 2015 ACMG/AMP BA1 threshold was AF >5%). The highest observed frequency for POLE c.2284C>T (p.Arg762Trp) is 0.00327% in South Asians (gnomAD v2.1, 1/30,616 alleles); overall AF is 0.0008% (2/251,424 alleles, gnomAD v2.1) and 0.00043% (7/1,613,882 alleles, gnomAD v4.1). All observed frequencies are 2-4 orders of magnitude below any BA1 threshold, so the variant is ultra-rare rather than common. The conclusion is robust to threshold choice because even the most lenient published BA1 cutoff (5%, PMID 25741868) is not approached.
Rule
BA1: allele frequency too high for the disorder. Project generic ACMG/AMP fallback threshold for non-VCEP genes: AF >1% in gnomAD (cf. Richards et al. 2015 ACMG/AMP, PMID 25741868, original BA1 exemplar AF >5%)
Evidence considered
gnomAD v2.1 total AF 7.95469e-06 (0.0008%, 2/251,424 alleles, 0 homozygotes); highest subpopulation South Asian AF 3.26627e-05 (0.0033%, 1/30,616 alleles) - far below the project generic-fallback BA1 threshold of AF >1% for non-VCEP gnomAD, anchored to the maximum credible population AF approach (Whiffin et al. 2017, PMID 28518168) and the ACMG/AMP BA1 definition (Richards et al. 2015, PMID 25741868)
gnomAD v4.1 total AF 4.33737e-06 (0.00043%, 7/1,613,882 alleles, 0 homozygotes), grpmax FAF 1.83e-06; highest subpopulation South Asian AF 1.09806e-05 (0.0011%, 1/91,070 alleles) - still far below the >1% BA1 threshold (Whiffin et al. 2017, PMID 28518168; Richards et al. 2015, PMID 25741868)
Still missing
gnomAD variant-level quality flags (e.g., inbreeding coefficient, FLAG status, raw depth) were not individually reviewed in the retrieved record; no frequency artifact is suspected but a direct QC-flag check would close this gap
gnomAD-Canada (HostSeq) registered as a source but not retrieved, so an independent Canadian population cohort was not available to corroborate the rarity estimate
BS1Not met: the highest allele frequency, 0.00327%, is about 100-fold below the >0.3% BS1 threshold.
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Reasoning
BS1 requires an allele frequency greater than expected for the disorder (project generic-fallback non-VCEP threshold AF >0.3% in gnomAD). The maximum AF anywhere is 0.00327% (South Asian, gnomAD v2.1) and the overall AFs are 0.0008% (v2.1) and 0.00043% (v4.1), ~100-fold below the BS1 threshold. POLE-associated polyposis/colorectal cancer predisposition is a rare autosomal dominant condition with incomplete penetrance, so even a maximum credible population AF computed from disease prevalence would be far below 0.3%; the observed AF does not exceed expected. BS1 is therefore not met in any ancestry group or dataset.
Rule
BS1: allele frequency greater than expected for the disorder. Project generic ACMG/AMP fallback threshold for non-VCEP genes: AF >0.3% in gnomAD (cf. Richards et al. 2015 ACMG/AMP, PMID 25741868; quantitative calibration per Whiffin et al. 2017, PMID 28518168)
Evidence considered
gnomAD v2.1: total AF 0.0008% (2/251,424), max subpopulation AF 0.0033% (SAS 1/30,616) - below the project generic-fallback BS1 threshold of AF >0.3% for non-VCEP gnomAD (Whiffin et al. 2017 maximum credible AF framework, PMID 28518168; Richards et al. 2015 BS1 definition, PMID 25741868)
gnomAD v4.1: total AF 0.00043% (7/1,613,882), max subpopulation AF 0.0011% (SAS 1/91,070), grpmax FAF 0.00018% - below the >0.3% BS1 threshold (Whiffin et al. 2017, PMID 28518168; Richards et al. 2015, PMID 25741868)
Still missing
No disease prevalence/penetrance estimate specific to POLE c.2284C>T was available to compute a formal maximum credible population AF, though the observed AF is far below even the most lenient fixed threshold
BS2Not met: no homozygotes and only 7 ultra-rare heterozygous carriers in 1.6 million gnomAD alleles, contrary to BS2's expected healthy-adult enrichment.
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Reasoning
BS2 requires the variant to be observed in healthy adult individuals (heterozygous for a dominant disorder, or homozygous for a recessive disorder) at a frequency inconsistent with the disease. For this dominant, adult-onset cancer-predisposition phenotype, the available population data show the opposite of BS2: 0 homozygotes in both gnomAD datasets (0/251,424 v2.1; 0/1,613,882 v4.1) and only 7 ultra-rare heterozygous carriers in 1.6M alleles (total AF 0.00043%). gnomAD is an unselected general-population cohort without phenotype verification, so it cannot by itself demonstrate observation in confirmed healthy adults, and no dedicated phenotype-verified healthy adult/control cohort (e.g., cancer-free adult controls) was present in the case evidence. BS2 is therefore not met on the available evidence.
Rule
BS2: variant observed in a healthy adult individual - heterozygous for a dominant disorder or homozygous for a recessive disorder, at a frequency inconsistent with disease (Richards et al. 2015 ACMG/AMP, PMID 25741868)
Evidence considered
gnomAD v2.1: 0 homozygotes in 251,424 alleles; 2 heterozygous carriers (AF 0.0008%) - no homozygous healthy carriers, inconsistent with BS2
gnomAD v4.1: 0 homozygotes in 1,613,882 alleles; 7 heterozygous carriers (AF 0.00043%) - absence of healthy homozygotes and near-absence of heterozygotes does not meet BS2 (Richards et al. 2015 BS2 definition, PMID 25741868)
No phenotype-verified healthy adult cohort data located in the case evidence bundle
Still missing
No phenotype-verified healthy adult control cohort (unaffected, cancer-free adults) was available; a dedicated control-cohort observation would be required to formally satisfy BS2 for this dominant adult-onset phenotype
gnomAD does not provide individual-level phenotype confirmation, limiting its use for BS2 to homozygote-count and allele-frequency checks
BP1Not met: POLE disease is driven by missense rather than truncating variants, so a missense change cannot receive BP1.
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Reasoning
BP1 (missense variant in a gene for which primarily truncating variants are known to cause disease) is not met. POLE disease causation is not primarily truncating: the established germline and somatic disease mechanisms are missense variants, principally within the exonuclease domain (León-Castillo et al. 2020: 'Pathogenic somatic missense mutations within the DNA polymerase epsilon (POLE) exonuclease domain define the important subtype of ultramutated tumours'), and germline POLE-predisposition phenotypes are associated with missense rather than null variants. The pvs1_gene_context artifact records LoF mechanism support (which concerns PVS1 eligibility for truncating variants under the generic framework) but does not establish truncating variants as the primary disease mechanism, and the framework notes explicitly state the gene context is not a basis for concluding truncating-primary causation. Because missense is a well-established mechanism of POLE disease, a missense variant cannot receive BP1. Status: not_met.
Rule
Generic ACMG/AMP 2015 BP1 (PMID 25741868); no POLE-specific BP1 specification in the governing custom framework
Evidence considered
vcep_path_250_323 - León-Castillo et al. 2020: pathogenic missense in the POLE exonuclease domain is causal for the POLE-ultramutated tumor phenotype, demonstrating missense (not truncating) is a primary mechanism of POLE disease
pvs1_gene_context - LoF mechanism supported for POLE (PVS1 eligibility context); does not indicate truncating variants are the primary/only mechanism, so it cannot support BP1
BP4Not met: REVEL 0.552 is far above the <=0.016 BP4 threshold, and SpliceAI shows no splice impact.
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Reasoning
The custom POLE framework BP4_Supporting rule (exact variant in Supplementary Table S2 or S3 with REVEL class 'Likely benign'/'Likely-benign' and >=4 benign in silico results) is not triggered because c.2284C>T/p.Arg762Trp is absent from both tables (verified directly in PATH-250-323-s003.xlsx and PATH-250-323-s004.xlsx), so generic in-silico fallback applies. Under generic fallback: REVEL = 0.552, which is far above the ClinGen SVI BP4 threshold of <= 0.016 (Pejaver et al. 2022, PMID 36413997), so REVEL provides no BP4 support. BayesDel 0.0523 is not usable (no verified published threshold). SpliceAI max delta = 0.00 indicates no predicted splice impact, but for a missense variant absence of predicted splice impact is not protein-level benign evidence and does not contribute to BP4 (the low-SpliceAI BP7 pathway is restricted to synonymous variants; Walker et al. 2023, PMID 37352859). No calibrated missense predictor supports BP4.
Rule
Custom POLE BP4 rule (exact variant in Supp Table S2/S3 + REVEL 'Likely benign' + >=4 benign tools) NOT triggered (variant absent); generic fallback: REVEL <=0.016 (PMID 36413997) required for BP4
Evidence considered
REVEL score 0.552 for NM_006231.4:c.2284C>T (p.Arg762Trp); ClinGen SVI calibration (Pejaver et al. 2022, Am J Hum Genet, PMID 36413997) recommends REVEL <=0.016 for BP4; 0.552 is far above this threshold -> no BP4 support.
BayesDel score 0.0523 (local lookup); no verified published calibration threshold (named publication and table) is available, so the score is treated as insufficiently calibrated and cannot support BP4.
SpliceAI max delta score = 0.00; absence of predicted splice impact does not constitute BP4 evidence for a missense variant (per ClinGen SVI Splicing Subgroup, PMID 37352859, low delta supports BP7 only for synonymous variants).
Custom POLE framework (PATH-250-323, Leon-Castillo et al. 2020) BP4_Supporting rule requires the exact variant in Supplementary Table S2 or S3 with REVEL class 'Likely benign' and >=4 benign in silico results; c.2284C>T/p.R762W is absent from both tables (verified by direct row inspection), so the rule is not triggered and generic fallback applies.
Still missing
Variant absent from Supplementary Tables S2/S3, so the table-grounded custom BP4 rule could not be applied
BayesDel score 0.0523 treated as insufficiently calibrated: no verified published threshold (PMID + table) available to this pipeline
No other calibrated missense predictor (e.g., aGVGD or a second meta-predictor with a published ClinGen-style calibration) available in this case
BP6Not met: no expert-panel Benign/Likely benign classification exists; ClinVar shows only Uncertain significance.
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Reasoning
BP6 was evaluated strictly per the group instruction: it may be triggered ONLY by an exact-variant ClinVar expert-panel classification of Benign/Likely benign; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger it. For NM_006231.4:c.2284C>T (ClinVar variation 420873), the record shows an aggregate classification of 'Uncertain significance' (2 stars), no expert-panel submissions (expert_panels empty), and three single-submitter laboratory VUS classifications (GeneDx, Labcorp/Invitae, Ambry). No expert-panel Benign/Likely benign classification exists for this exact variant, so BP6 is not met.
Rule
Generic ACMG/AMP 2015 BP6 (reputable source recently reports variant as benign, evidence not available to the laboratory for independent evaluation), restricted per group instruction to exact-variant ClinVar expert-panel Benign/Likely benign classifications only.
Evidence considered
clinvar
generic_acmg_combination_rules
Still missing
No ClinVar expert-panel (3-star) Benign/Likely benign classification exists for this variant
Aggregate 2-star VUS status cannot be used as a benign assertion under the group rule
PS2Not assessed: no proband-parent trio or de novo occurrence data were available.
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Reasoning
No de novo occurrence data exist anywhere in the case evidence bundle. No proband-parental trio data, parental test results, or maternity/paternity confirmation are reported for POLE NM_006231.4:c.2284C>T (p.Arg762Trp) in ClinVar (VCV000420873; 3 germline submissions, all Uncertain significance), in either retrieved publication, or in any other bundle source. The governing POLE framework (León-Castillo et al. 2020 custom framework, vcep_path_250_323) customizes only PM1/PS4/PP3/BP4, so PS2 is governed by generic ACMG/AMP 2015 (Richards et al., PMID 25741868), which requires a documented de novo variant with confirmed maternity and paternity. With no trio/parental testing evidence, PS2 cannot be evaluated and is returned as not_assessed.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): PS2 = de novo variant with confirmed maternity and paternity. The custom POLE framework (León-Castillo et al. 2020, vcep_path_250_323) customizes only PM1/PS4/PP3/BP4 and does not alter PS2.
Evidence considered
clinvar (VCV000420873): 3 germline submissions (GeneDx SCV000569891, Labcorp/Invitae SCV001223981, Ambry SCV005928891), all Uncertain significance, 2-star aggregate; no de novo, parental-testing, or trio assertions present in retrieved submission data.
PMID:28492532 (Sherloc, Nykamp et al. 2017): cited by Labcorp submission; full-text file in case bundle is empty (0 bytes); no variant-specific data extractable.
PMID:25394175 (Hampel et al. 2015 ACMG referral-indications guideline): reviewed; contains no variant-specific or de novo data.
generic_acmg_combination_rules (Richards et al. 2015, PMID 25741868): governs PS2 because the custom POLE framework does not customize de novo criteria.
Still missing
No proband-parent trio or parental-testing data available in any case source; a de novo occurrence with confirmed maternity/paternity cannot be confirmed or excluded.
Requires trio exome/genome or parental Sanger/orthogonal genotyping of the proband's parents showing absence of the variant in both parents (with maternity/paternity confirmed).
PS3Not assessed: no functional assay evidence for this variant was available. Flagged for human review: a laboratory submission cites published functional studies without a PMID, which could not be verified.
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Reasoning
No functional assay evidence for POLE p.Arg762Trp (c.2284C>T) is present in the case bundle, so PS3 cannot be assessed. The applicable local POLE framework (León-Castillo et al. 2020 custom framework, vcep_path_250_323) customizes only PM1, PS4, PP3 and BP4 and defines no PS3 rule; under generic ACMG/AMP 2015 (PMID 25741868, registry key generic_acmg_combination_rules), PS3 requires well-established functional studies showing a deleterious effect. OncoKB (registry key oncokb) explicitly states it 'did not identify variant-specific reviewed functional evidence for this variant' (classification 'Unknown Oncogenic Effect', is_variant_specific=false, not_reviewed=true). The only PS3 lead in the case is auto-parsed assertion text from the GeneDx submission SCV000569891 (ClinVar variation 420873) referencing 'published functional studies'; that submission carries no PMIDs (rejection reason no_valid_pmids, usable_for_criterion_leads=false) and the sentence is a generic laboratory template, so per policy it cannot be used to infer PS3 from another source's assertion or classification. In silico predictors (REVEL 0.552, BayesDel 0.0523) and SpliceAI (max delta 0.00) are computational, not functional assays, and are not PS3 evidence. R762 lies in the polymerase (catalytic) domain, outside the exonuclease-domain scope of the local hotspot framework. A human reviewer should follow up the GeneDx assertion text to determine whether a citable functional study of this exact variant exists.
Still missing
No validated functional assay evidence for the exact variant p.Arg762Trp (e.g., yeast-based POLE polymerase/exonuclease activity assay, cell-based replication or POLE-ultramutation/signature functional readout) with documented assay controls and biological relevance to the POLE disease mechanism
GeneDx SCV000569891 assertion text mentions 'published functional studies' without a citation; the underlying study must be located, verified to test this exact variant, and assessed for assay quality before PS3 could be applied
No POLE-specific VCEP/CSPEC PS3 specification or strength calibration is available; only generic ACMG/AMP 2015 PS3 (PMID 25741868) applies, and no functional data exist to trigger it
PM3Not assessed: no phase, pedigree, or proband genotype data were available to evaluate a trans arrangement.
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Reasoning
PM3 (generic ACMG/AMP 2015: for recessive disorders, detected in trans with a pathogenic variant) cannot be adjudicated because the case bundle contains no phase, pedigree, or proband genotype data. The governing framework is the local custom POLE framework (Leon-Castillo et al. 2020), which specifies rules only for PM1, PS4, PP3 and BP4; PM3 is not customized, so the generic definition applies (Richards et al. 2015, PMID 25741868). ClinVar record 420873 (3 germline submissions, all 'Uncertain significance', criteria provided/single submitter, no expert panel) reports no biallelic occurrence, no second allele, and no phase. gnomAD v2.1 (2/251,424) and v4.1 (7/1,613,882) show zero homozygotes. Both retrieved publications (PMID:25394175, PMID:28492532) were full-text searched and do not mention c.2284C>T / p.(Arg762Trp) or any trans observation. POLE germline cancer predisposition (polymerase proofreading-associated polyposis, OMIM 615083) is autosomal dominant; although a recessive POLE phenotype exists (FILS syndrome, OMIM 615139), nothing in the case materials links this variant to a recessive presentation or to a pathogenic variant in trans. Evidence is insufficient to apply or refute PM3.
Rule
Generic ACMG/AMP 2015 PM3: 'For recessive disorders, detected in trans with a pathogenic variant' (Richards et al., PMID 25741868). No PM3 specification exists in the governing Leon-Castillo 2020 custom POLE framework (which customizes PM1, PS4, PP3, BP4 only), so generic ACMG/AMP applies.
Evidence considered
Generic ACMG/AMP 2015 PM3 definition (Richards et al. 2015, PMID 25741868; source_registry key 'generic_acmg_combination_rules'): 'For recessive disorders, detected in trans with a pathogenic variant.' The governing Leon-Castillo 2020 custom POLE framework customizes only PM1/PS4/PP3/BP4 and contains no PM3 specification.
ClinVar record 420873 (source_registry key 'clinvar'): 3 germline submissions, all Uncertain significance, single-submitter review status, no expert panel; no phase, no second allele, and no biallelic observation reported. Consulted only to confirm absence of phase data; no classification inference drawn from it.
gnomAD v2.1 and v4.1: total allele counts 2/251,424 and 7/1,613,882 respectively with homozygotes = 0 in both; no homozygous observation that could support a recessive/trans configuration.
PMID:25394175 and PMID:28492532: full texts searched for the variant and for phase/trans/cis content; neither mentions POLE c.2284C>T / p.(Arg762Trp) nor provides any proband or phase information.
Still missing
No family/pedigree or phase data (trans vs cis) for any proband carrying this variant
No second POLE variant identified; no pathogenic variant documented in trans
Recessive-context applicability (e.g., FILS syndrome) not assessable from case materials
No affected-proband observations with biallelic POLE variants in the retrieved literature
PM5Not assessed: no pathogenic comparator missense at Arg762 was identified; the required same-residue survey is pending human review.
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Reasoning
PM5 (novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before) cannot be assessed from the collected evidence. The pipeline's PM5 candidate artifact (output/pm5_candidates.json, registry key pm5_candidates) reports pm5_mode 'unknown' and 'eligible_for_classic_pm5_search: false' because 'Unable to confirm classic same-residue PM5 semantics safely; skipping automatic candidate harvesting.' It collected 0 candidates of any kind (total_candidates_seen 0, same_residue_candidates 0, expert_panel_plp_candidates 0) and its recommendation explicitly states 'Review whether any collected same-residue comparator variants satisfy the governing PM5 rule; do not apply PM5 from this artifact alone.' No comparator pathogenic missense at Arg762 (e.g., p.Arg762Gly/Ser/Gln/Pro/Leu) was identified in any collected source, but a dedicated same-residue survey (ClinVar/LOVD/literature search for other substitutions at residue 762) was not performed, so the absence of a comparator cannot be asserted with confidence. The two retrieved publications contain no variant-specific content and do not contribute. Status is therefore not_assessed pending a manual same-residue comparator search.
Rule
Generic ACMG/AMP 2015 PM5 (PMID 25741868); no POLE-specific PM5 specification in the governing custom framework
Evidence considered
pm5_candidates - output/pm5_candidates.json: pm5_mode 'unknown', same_residue_candidates 0, total_candidates_seen 0; recommendation level 'not_applicable'; artifact instructs manual review and not to apply PM5 from the artifact alone
clinvar - ClinVar variation 420873 (exact variant match only); no same-residue comparator submissions surfaced in the collected record
PMID:25394175 and PMID:28492532 - full texts searched; no same-residue comparator or variant-specific content
Generic ACMG/AMP 2015 PM5 rule (Richards et al. 2015, PMID 25741868) as the governing rule definition
Still missing
No dedicated survey of other amino-acid substitutions at POLE residue 762 (e.g., ClinVar/LOVD/literature search for p.Arg762Gly/Ser/Gln/Pro/Leu or any pathogenic missense at codon 762)
pm5_candidates.json harvest mode is 'unknown' with 0 candidates; automatic harvesting was skipped, requiring manual review before PM5 can be met or excluded
PM6Not assessed: no evidence of a de novo occurrence, with or without confirmed parentage, was available.
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Reasoning
No de novo occurrence data of any kind exist for this variant. There is no evidence that the variant arose de novo (with or without confirmed parentage), no proband-parent testing results, and no mosaicism assessment. ClinVar submissions for VCV000420873 report no family or inheritance details beyond germline origin. Because the custom POLE framework does not address PM6, generic ACMG/AMP 2015 (Richards et al., PMID 25741868) applies: PM6 requires an assumed de novo occurrence without confirmation of maternity and paternity. With no such data, PM6 cannot be evaluated and is returned as not_assessed.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): PM6 = assumed de novo without confirmation of maternity and paternity. The custom POLE framework does not customize PM6.
Evidence considered
clinvar (VCV000420873): germline submissions only; no de novo or parental-testing assertions retrieved.
PMID:28492532 (Sherloc): full text empty in case bundle; no variant-specific data.
PMID:25394175 (ACMG referral guideline): no variant-specific data.
generic_acmg_combination_rules (Richards et al. 2015, PMID 25741868): governs PM6 in the absence of a POLE-specific specification.
Still missing
No de novo occurrence data at all (neither with nor without parentage confirmation) available in any case source.
Requires proband-parent genotyping showing absence of the variant in both parents, even where maternity/paternity is not formally confirmed.
PP1Not assessed: no family segregation data were available.
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Reasoning
No segregation data exist for this variant. No affected family members were tested, no meioses were counted, and no co-segregation or non-segregation observations are reported in any bundle source. The custom POLE framework (León-Castillo et al. 2020) does not specify PP1, so generic ACMG/AMP 2015 (Richards et al., PMID 25741868) applies: PP1 requires co-segregation of the variant with disease in multiple affected family members in a gene definitively known to cause the disease. With no segregation data, PP1 cannot be evaluated and is returned as not_assessed.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): PP1 = co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. The custom POLE framework does not customize PP1.
Evidence considered
clinvar (VCV000420873): no segregation or family-testing assertions in retrieved submission data.
PMID:28492532 (Sherloc): full text empty in case bundle; no variant-specific data.
PMID:25394175 (ACMG referral guideline): no variant-specific data.
generic_acmg_combination_rules (Richards et al. 2015, PMID 25741868): governs PP1 in the absence of a POLE-specific specification.
Still missing
No co-segregation data in affected family members (no affected relatives tested, no meioses counted).
Requires segregation testing of affected relatives of the proband; the number of informative meioses would determine strength if data become available.
PP2Not assessed: no gene-level missense constraint metric (e.g., gnomAD Z-score) was available to establish a low rate of benign missense variation.
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Reasoning
PP2 requires BOTH (a) a gene with a low rate of benign missense variation and (b) missense as a common mechanism of disease. Component (b) is supported for POLE: germline POLE-associated disease (polymerase proofreading-associated polyposis / colorectal cancer predisposition, FAP-like phenotypes) and the POLE-ultramutated tumor phenotype are driven predominantly by missense variants in the exonuclease domain, consistent with the León-Castillo 2020 framework (pathogenic somatic missense in the exonuclease domain defines the POLE-ultramutated subtype) and with the gene-context artifact (pvs1_gene_context) confirming a disease mechanism for POLE. Component (a) is NOT documented in this case's evidence: no gene-level missense constraint metric (e.g., gnomAD missense Z-score or observed/expected missense ratio with a named publication), no ClinGen gene-disease curation summary, and no HCI prior (hci_prior found false, gene_not_supported) were retrieved. Without a verifiable low-rate-of-benign-missense basis, PP2 cannot be met under generic ACMG/AMP 2015, and the criterion is returned as not_assessed rather than met on the strength of the mechanism component alone. The variant-level rarity in gnomAD (AF ~4.3e-6 to 8.0e-6, 0 homozygotes) is variant-level evidence and does not substitute for the gene-level benign-missense-rate requirement of PP2.
Rule
Generic ACMG/AMP 2015 PP2 (PMID 25741868); no POLE-specific PP2 specification in the governing custom framework
Evidence considered
vcep_path_250_323 - León-Castillo et al. 2020: pathogenic missense in the POLE exonuclease domain is the established mechanism of the POLE-ultramutated phenotype (supports the missense-common-mechanism component of PP2)
pvs1_gene_context - gene-level PVS1 eligibility context confirming a POLE disease mechanism (LoF mechanism supported); does not itself quantify benign missense variation
gnomad_v2 / gnomad_v4 - variant-level population data (AF 7.95e-6 / 4.34e-6, 0 homozygotes); noted as not sufficient for the gene-level PP2 benign-missense-rate requirement
Gene-level missense constraint data for POLE (e.g., gnomAD missense Z-score / observed-expected missense ratio with a named publication, or a ClinGen gene-disease curation asserting low benign missense variation) is absent from the case evidence and must be retrieved before PP2 can be adjudicated
PP4Not assessed: no proband phenotype or family-history data were available to establish phenotype specificity.
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Reasoning
PP4 (generic ACMG/AMP 2015: phenotype or family history highly specific for a disease with a single genetic etiology) cannot be evaluated because the case bundle contains no proband-level clinical data: no personal cancer/polyposis history, no tumor phenotype (e.g., endometrial carcinoma or colorectal polyposis consistent with polymerase proofreading-associated polyposis), and no family history or segregation context. The only phenotypic strings available are the ClinVar condition labels 'Hereditary cancer-predisposing syndrome' and 'not provided', which are nonspecific and cannot establish phenotype specificity for POLE. No proband phenotype or family-history evidence is therefore available to adjudicate PP4; the criterion is left not_assessed pending clinical case data.
Rule
Generic ACMG/AMP 2015 PP4: phenotype or family history highly specific for a disease with a single genetic etiology (Richards et al. 2015, PMID 25741868). Not customized by the local POLE framework.
Evidence considered
clinvar
generic_acmg_combination_rules
Still missing
No proband clinical phenotype or family history data are present in the case evidence bundle
ClinVar condition labels ('Hereditary cancer-predisposing syndrome', 'not provided') are nonspecific and insufficient to support a POLE-specific phenotype assertion
No case reports, tumor pathology, or personal/family cancer history are available to evaluate phenotype specificity
BS3Not assessed: no functional assay evidence showing a lack of damaging effect was available.
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Reasoning
BS3 cannot be assessed because no functional assay evidence showing a lack of damaging effect exists for POLE p.Arg762Trp in the case bundle. Generic ACMG/AMP 2015 (PMID 25741868, registry key generic_acmg_combination_rules) defines BS3 as well-established functional studies showing no damaging effect (Sherloc, PMID 28492532, describes the same rule as 'well-established assay, no deleterious effect'); the local León-Castillo POLE framework defines no BS3 rule. OncoKB provides no variant-specific functional evidence of any direction. Population-frequency data (gnomAD v2.1 AF 7.95e-06, 2/251424 alleles) and in silico scores are not functional evidence and cannot substitute for BS3. No assay, control, or calibration data are available, so BS3 is not_met-or-benign evidence is entirely absent.
Still missing
No functional assay demonstrating wild-type-level function / no damaging effect for the exact variant p.Arg762Trp (e.g., polymerase activity comparable to wild-type in a validated assay) with assay controls
No applicable POLE-specific BS3 specification or assay-calibration data
No ClinVar expert-panel or otherwise validated functional assessment of this variant (submission audit: expert_panel_submissions=0)
BS4Not assessed: no segregation data were available to test for lack of segregation in affected family members.
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Reasoning
No family segregation data exist that could demonstrate lack of segregation. There are no affected-family-member genotyping results, no unaffected-carrier observations, and no non-segregation events reported for POLE NM_006231.4:c.2284C>T in any bundle source. The custom POLE framework does not specify BS4, so generic ACMG/AMP 2015 (Richards et al., PMID 25741868) applies: BS4 requires lack of segregation in affected members of a family (or the variant observed where segregation would exclude it). BS4 cannot be positively evaluated and is returned as not_assessed; it must not be inferred from the mere absence of segregation data.
Rule
Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): BS4 = lack of segregation in affected members of a family. The custom POLE framework does not customize BS4.
Evidence considered
clinvar (VCV000420873): no non-segregation or family-testing assertions in retrieved submission data.
PMID:28492532 (Sherloc): full text empty in case bundle; no variant-specific data.
PMID:25394175 (ACMG referral guideline): no variant-specific data.
generic_acmg_combination_rules (Richards et al. 2015, PMID 25741868): governs BS4 in the absence of a POLE-specific specification.
Still missing
No segregation testing results in affected or unaffected relatives; lack of segregation cannot be demonstrated.
Requires genotyping of affected relatives (and informative unaffected relatives) in families of probands carrying the variant.
BP2Not assessed: no phase data relative to another variant were available.
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Reasoning
BP2 (generic ACMG/AMP 2015: observed in trans with a pathogenic variant for a fully dominant disease/disorder, or observed in cis with a pathogenic variant in any inheritance pattern) requires experimentally determined phase, which is entirely absent from the case bundle. The governing local custom POLE framework (Leon-Castillo et al. 2020) specifies no BP2 rule, so the generic definition applies (Richards et al. 2015, PMID 25741868). No pedigree or familial segregation data are available; none of the 3 ClinVar germline submissions (all Uncertain significance) report phase or co-occurring variants; and both retrieved publications (PMID:25394175, PMID:28492532) were full-text searched and contain no mention of this variant or any cis/trans observation. Without phase determination relative to any other variant, BP2 can be neither met nor refuted.
Rule
Generic ACMG/AMP 2015 BP2: 'Observed in trans with a pathogenic variant for a fully dominant disease/disorder; or observed in cis with a pathogenic variant in any inheritance pattern' (Richards et al., PMID 25741868).
Evidence considered
Generic ACMG/AMP 2015 BP2 definition (Richards et al. 2015, PMID 25741868; source_registry key 'generic_acmg_combination_rules'): 'Observed in trans with a pathogenic variant for a fully dominant disease/disorder; or observed in cis with a pathogenic variant in any inheritance pattern.' The governing Leon-Castillo 2020 custom POLE framework contains no BP2 specification.
ClinVar record 420873 (source_registry key 'clinvar'): no phase or co-occurring-variant information reported in any of the 3 germline submissions.
PMID:25394175 and PMID:28492532: full texts searched; neither mentions POLE c.2284C>T / p.(Arg762Trp) and neither reports any cis/trans observation.
Still missing
No phase determination (cis vs trans) of this variant relative to any other variant
No familial/pedigree or segregation data in the case bundle
No documented pathogenic variant co-occurring in the same individual for cis/trans analysis
BP5Not assessed: no case-level data on an alternate molecular basis of disease were available.
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Reasoning
BP5 (generic ACMG/AMP 2015: variant found in a case with an alternate molecular basis for disease) requires proband-level evidence that the individual carrying the variant has an established alternative etiology (e.g., a pathogenic variant in another gene or a non-genetic cause). The case bundle contains no proband case data whatsoever: no index-case report, no co-occurring pathogenic variants, no tumor molecular findings. The ClinVar submissions provide germline testing classifications only and contain no alternate-cause documentation. With no case-level information, BP5 cannot be assessed and is left not_assessed pending case data.
Rule
Generic ACMG/AMP 2015 BP5: variant found in a case with an alternate molecular basis for disease (Richards et al. 2015, PMID 25741868). Not customized by the local POLE framework.
Evidence considered
generic_acmg_combination_rules
Still missing
No proband-level case data in the bundle with which to evaluate an alternate molecular basis of disease
No documented co-occurring pathogenic variant or alternative etiology for the variant carrier is available
Not applicable · 4· recorded as not applicableShow reasons ▾Hide reasons ▴PVS1N/ANot applicable: this is a missense change, and PVS1 applies only to null variants such as nonsense, frameshift, or splice-site changes.
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Reasoning
NM_006231.4:c.2284C>T is a single-nucleotide substitution predicted by Mutalyzer and VariantValidator to cause a missense change NP_006222.2:p.(Arg762Trp) in exon 20 of 49 of the MANE Select transcript NM_006231.4. PVS1 under the governing generic ClinGen SVI framework (PMC6185798) applies only to null variants (nonsense, frameshift, canonical +/-1,2 splice-site, initiation codon, single/multi-exon deletions). The pipeline variant-level assessment (pvs1_variant_assessment.json) classified the consequence as 'missense', canonical_splice_consensus=false, variant_bucket='other', and did not apply the generic PVS1 framework. SpliceAI reports max delta score = 0.00, providing no evidence of a splice-mediated null consequence. Although pvs1_gene_context.json supports POLE loss of function as a germline disease mechanism (making generic PVS1 adjudication eligible in principle), gene-level eligibility does not change the variant class; a missense substitution cannot satisfy any PVS1 null-variant condition. The criterion is therefore not applicable. No final classification from ClinVar or any other source was used to reach this conclusion.
Rule
Generic ClinGen SVI PVS1 recommendations (PMC6185798): PVS1 applies to null variants (nonsense, frameshift, canonical +/-1,2 splice, initiation codon, single/multi-exon deletion); missense variants are outside scope. No POLE-specific PVS1 specification exists in the local custom framework (which customizes only PM1, PS4, PP3, BP4).
Evidence considered
Variant annotation from Mutalyzer/VariantValidator (prefetch.json normalize step): NM_006231.4:c.2284C>T -> p.(Arg762Trp), missense, exon 20 of 49, MANE Select transcript NM_006231.4 (CDS 1-6861, 2286-residue protein)
pvs1_variant_assessment.json: consequence_class='missense', canonical_splice_consensus=false, variant_bucket='other', apply_generic_pvs1_framework=false, framework_source=ClinGen SVI PVS1 recommendations (PMC6185798)
pvs1_gene_context.json: POLE germline LoF mechanism supported (pvs1_gene_gate='eligible') but this only establishes eligibility, not applicability to a missense variant
SpliceAI (evidence.json): max delta score = 0.00, no predicted splice impact (no threshold applied; used only as corroboration that no splice-mediated null consequence exists)
ClinVar record 420873 annotation 'NM_006231.4(POLE):c.2284C>T (p.Arg762Trp)' used solely to confirm the missense consequence; ClinVar classification (Uncertain significance) was not used
PM4N/ANot applicable: this missense change preserves the reading frame and protein length.
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Reasoning
PM4 addresses protein length change resulting from in-frame deletions/insertions in a nonrepeat region or from stop-loss variants. The queried variant is a single-nucleotide substitution causing a missense change p.(Arg762Trp); the open reading frame is preserved, no residues are inserted or deleted, and the protein length is unchanged (2286 amino acids for NP_006222.2, CDS 1-6861 of NM_006231.4). Because the variant class cannot produce a protein length change, PM4 is not applicable under generic ACMG/AMP 2015 (PMID 25741868). No variant annotation in the evidence bundle (Mutalyzer, VariantValidator, ClinVar record 420873) indicates an in-frame indel or stop-loss consequence.
Rule
Generic ACMG/AMP 2015 (PMID 25741868): PM4 applies to in-frame deletions/insertions in a nonrepeat region or stop-loss variants that alter protein length; a missense substitution is outside scope. The local custom POLE framework does not customize PM4.
Evidence considered
ACMG/AMP 2015 (Richards et al., PMID 25741868; registered as generic_acmg_combination_rules): PM4 = protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
BP3N/ANot applicable: the variant is a single-nucleotide substitution, not an in-frame indel in a repeat region.
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Reasoning
BP3 addresses in-frame deletions/insertions located in a repetitive region without a known function. The queried variant is a single-nucleotide substitution (missense p.(Arg762Trp)), not an indel, and no repeat-region context is reported for exon 20/c.2284 in any source in the evidence bundle (Cancer Hotspots reports no statistically significant hotspot at POLE R762; no repeat annotation appears in the variant data). BP3 is therefore not applicable under generic ACMG/AMP 2015 (PMID 25741868).
Rule
Generic ACMG/AMP 2015 (PMID 25741868): BP3 applies to in-frame deletions/insertions in a repetitive region without a known function; a missense SNV is outside scope. The local custom POLE framework does not customize BP3.
Evidence considered
ACMG/AMP 2015 (Richards et al., PMID 25741868; registered as generic_acmg_combination_rules): BP3 = in-frame deletions/insertions in a repetitive region without a known function
Variant annotation (prefetch.json): single-nucleotide substitution, not an indel; no repeat-region context available for this variant
BP7N/ANot applicable: BP7 applies only to synonymous variants, and this is a missense change.
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Reasoning
BP7 applies only to synonymous (silent) variants for which splicing prediction algorithms do not predict an impact on the splice consensus sequence or creation of a new splice site. NM_006231.4:c.2284C>T is a missense variant (NP_006222.2:p.Arg762Trp, exon 20), not a synonymous variant, so BP7 cannot be applied regardless of the SpliceAI result (max delta = 0.00).
Rule
Generic ACMG BP7: synonymous variant with no predicted splice impact (e.g., SpliceAI delta <0.1 per ClinGen SVI Splicing Subgroup, PMID 37352859); not applicable to missense variants
Evidence considered
SpliceAI max delta score = 0.00 for NM_006231.4:c.2284C>T; noted for completeness, but BP7 is not applicable because the variant is missense (p.Arg762Trp), not synonymous.
AF 4.3e-06 · 7 / 1,613,882 alleles · 0 hom · FAF 1.8e-06
South Asian1 / 91,070
1.1e-05
European (non-Finnish)6 / 1,179,976
5.1e-06
0 alternate alleles recorded in 8 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American.
gnomAD v2.1
AF 8e-06 · 2 / 251,424 alleles · 0 hom
South Asian1 / 30,616
3.3e-05
European (non-Finnish)1 / 113,704
8.8e-06
0 alternate alleles recorded in 6 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals.
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 4.33737e-06; MAF= 0.00043%, 7/1613882 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09806e-05; MAF= 0.00110%, 1/91070 alleles, homozygotes = 0); grpmax FAF= 1.83e-06.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 7.95469e-06; MAF= 0.00080%, 2/251424 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26627e-05; MAF= 0.00327%, 1/30616 alleles, homozygotes = 0).
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Pangolin splice lossmagnitude shown
-0.010
Pangolin splice gain
0.000
Other predictors
REVEL
0.552
BayesDel
0.052
How the predictions were used
PP3Not met: REVEL 0.552 falls in the indeterminate range (PP3 requires >=0.932), and SpliceAI max delta 0.00 shows no splice impact.
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Reasoning
Variant NM_006231.4:c.2284C>T (POLE, p.Arg762Trp) is a missense variant in exon 20. The governing local custom POLE framework (Leon-Castillo et al. 2020, PATH-250-323) pre-assigns PP3_Supporting only when the exact variant appears in Supplementary Table S2 or S3 with REVEL class 'likely disease causing' and <=1 benign in silico result; direct inspection of PATH-250-323-s003.xlsx (Table S2) and PATH-250-323-s004.xlsx (Table S3) shows the variant is absent from both tables (and from Table S1), so the custom rule is not triggered and the framework mandates fallback to the generic in-silico workflow. Under generic fallback: (1) REVEL score = 0.552; per ClinGen SVI calibration (Pejaver et al. 2022, PMID 36413997) REVEL >= 0.932 supports PP3 and <= 0.016 supports BP4, so 0.552 lies in the indeterminate range and provides no PP3 support; (2) SpliceAI max delta = 0.00 (pangolin_SG 0.0, pangolin_SL -0.01), well below the delta >= 0.2 splice-impact threshold of the ClinGen SVI Splicing Subgroup (Walker et al. 2023, PMID 37352859), so the splice path provides no PP3 support; (3) BayesDel score = 0.0523 cannot be used because no verified published calibration threshold (publication + table) is available, per pipeline policy. No computational evidence path meets the PP3 threshold.
Rule
Custom POLE PP3 rule (exact variant in Supp Table S2/S3 + REVEL 'likely disease causing' + <=1 benign tool) NOT triggered (variant absent); generic fallback: REVEL >=0.932 (PMID 36413997) or SpliceAI delta >=0.2 (PMID 37352859) required for PP3
Evidence considered
REVEL score 0.552 for NM_006231.4:c.2284C>T (p.Arg762Trp); ClinGen SVI calibration (Pejaver et al. 2022, Am J Hum Genet, PMID 36413997) recommends REVEL >=0.932 for PP3 and <=0.016 for BP4; 0.552 is indeterminate -> no PP3 support.
SpliceAI max delta score = 0.00 (pangolin_SG 0.0, pangolin_SL -0.01); ClinGen SVI Splicing Subgroup recommendations (Walker et al. 2023, Am J Hum Genet, PMID 37352859) require delta >=0.2 for splice-impact PP3; 0.00 provides no PP3 support.
BayesDel score 0.0523 (local lookup); no verified published calibration threshold (named publication and table) is available, so the score is treated as insufficiently calibrated and cannot support PP3.
Custom POLE framework (PATH-250-323, Leon-Castillo et al. 2020) PP3_Supporting rule requires the exact variant in Supplementary Table S2 or S3 with REVEL class 'likely disease causing' and <=1 benign in silico result; c.2284C>T/p.R762W is absent from PATH-250-323-s003.xlsx and PATH-250-323-s004.xlsx (verified by direct row inspection), so the rule is not triggered and generic fallback applies.
Still missing
Variant absent from POLE framework Supplementary Tables S2/S3, so the table-grounded custom PP3 rule could not be applied
BayesDel score 0.0523 treated as insufficiently calibrated: no verified published threshold (PMID + table) available to this pipeline
REVEL 0.552 falls in the ClinGen SVI indeterminate range (0.016-0.932), providing no PP3 support
BP4Not met: REVEL 0.552 is far above the <=0.016 BP4 threshold, and SpliceAI shows no splice impact.
Details ▾Hide ▴
Reasoning
The custom POLE framework BP4_Supporting rule (exact variant in Supplementary Table S2 or S3 with REVEL class 'Likely benign'/'Likely-benign' and >=4 benign in silico results) is not triggered because c.2284C>T/p.Arg762Trp is absent from both tables (verified directly in PATH-250-323-s003.xlsx and PATH-250-323-s004.xlsx), so generic in-silico fallback applies. Under generic fallback: REVEL = 0.552, which is far above the ClinGen SVI BP4 threshold of <= 0.016 (Pejaver et al. 2022, PMID 36413997), so REVEL provides no BP4 support. BayesDel 0.0523 is not usable (no verified published threshold). SpliceAI max delta = 0.00 indicates no predicted splice impact, but for a missense variant absence of predicted splice impact is not protein-level benign evidence and does not contribute to BP4 (the low-SpliceAI BP7 pathway is restricted to synonymous variants; Walker et al. 2023, PMID 37352859). No calibrated missense predictor supports BP4.
Rule
Custom POLE BP4 rule (exact variant in Supp Table S2/S3 + REVEL 'Likely benign' + >=4 benign tools) NOT triggered (variant absent); generic fallback: REVEL <=0.016 (PMID 36413997) required for BP4
Evidence considered
REVEL score 0.552 for NM_006231.4:c.2284C>T (p.Arg762Trp); ClinGen SVI calibration (Pejaver et al. 2022, Am J Hum Genet, PMID 36413997) recommends REVEL <=0.016 for BP4; 0.552 is far above this threshold -> no BP4 support.
BayesDel score 0.0523 (local lookup); no verified published calibration threshold (named publication and table) is available, so the score is treated as insufficiently calibrated and cannot support BP4.
SpliceAI max delta score = 0.00; absence of predicted splice impact does not constitute BP4 evidence for a missense variant (per ClinGen SVI Splicing Subgroup, PMID 37352859, low delta supports BP7 only for synonymous variants).
Custom POLE framework (PATH-250-323, Leon-Castillo et al. 2020) BP4_Supporting rule requires the exact variant in Supplementary Table S2 or S3 with REVEL class 'Likely benign' and >=4 benign in silico results; c.2284C>T/p.R762W is absent from both tables (verified by direct row inspection), so the rule is not triggered and generic fallback applies.
Still missing
Variant absent from Supplementary Tables S2/S3, so the table-grounded custom BP4 rule could not be applied
BayesDel score 0.0523 treated as insufficiently calibrated: no verified published threshold (PMID + table) available to this pipeline
No other calibrated missense predictor (e.g., aGVGD or a second meta-predictor with a published ClinGen-style calibration) available in this case
BP7N/ANot applicable: BP7 applies only to synonymous variants, and this is a missense change.
Details ▾Hide ▴
Reasoning
BP7 applies only to synonymous (silent) variants for which splicing prediction algorithms do not predict an impact on the splice consensus sequence or creation of a new splice site. NM_006231.4:c.2284C>T is a missense variant (NP_006222.2:p.Arg762Trp, exon 20), not a synonymous variant, so BP7 cannot be applied regardless of the SpliceAI result (max delta = 0.00).
Rule
Generic ACMG BP7: synonymous variant with no predicted splice impact (e.g., SpliceAI delta <0.1 per ClinGen SVI Splicing Subgroup, PMID 37352859); not applicable to missense variants
Evidence considered
SpliceAI max delta score = 0.00 for NM_006231.4:c.2284C>T; noted for completeness, but BP7 is not applicable because the variant is missense (p.Arg762Trp), not synonymous.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.552. BayesDel score = 0.0522946.
2 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Recorded publications
A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment.
Hampel H et al. · 2015
Hampel et al. 2015 is an ACMG/NSGC practice guideline defining referral indications for cancer predisposition assessment. It is cited in the ClinVar record for this variant but is a clinical referral guideline with no variant-specific content; it contains no de novo, segregation, or family-testing data relevant to POLE c.2284C>T. Not usable for PS2, PM6, PP1, or BS4.
Consider referral for a cancer genetic consultation if your patient or any of their first-degree relatives meet any of these referral criteria.
publications/25394175.txt, guideline purpose statement (opening section, near doi:10.1038/gim.2014.147)
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
Nykamp K et al. · 2017
Sherloc (Nykamp et al. 2017), a refinement of the ACMG/AMP variant classification criteria, is cited by the Labcorp ClinVar submission for this variant. The full-text file for this PMID in the case bundle is empty (0 bytes), so no framework text could be reviewed and no variant-specific de novo or segregation evidence is available. It contributes nothing to PS2, PM6, PP1, or BS4 adjudication.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 4.33737e-06; MAF= 0.00043%, 7/1613882 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09806e-05; MAF= 0.00110%, 1/91070 alleles, homozygotes = 0); grpmax FAF= 1.83e-06.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 7.95469e-06; MAF= 0.00080%, 2/251424 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26627e-05; MAF= 0.00327%, 1/30616 alleles, homozygotes = 0).
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories). (ClinVarID = 420873)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.552. BayesDel score = 0.0522946.
Functional
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. POLE, the catalytic subunit of DNA polymerase epsilon, is an enzyme involved in DNA replication and repair. Select POLE mutations lead to ultra-high m
Somatic
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57690452, n = 1 times).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
This variant was interpreted by pipeline 7.1.0.
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